The G.F.S. Aegis and various Federation Starfighters engage the pirate forces creating a diversion, which allows a small dropship carrying the Federation Force to get near the force field so that the soldiers can blast out and through the force field. After a number of intense battles with scores of Space Pirates, the Force continues onward.

Further inside the Doomseye, the Force discovers what happened to Samus Aran after the Federation lost contact with her: she was abducted and taken aboard the Doomseye. She is hit with an amplification beam, increasing her size and brainwashing her into fighting the Federation Force in her Morph Ball form. They are forced to defeat Samus, who is crushed under debris following the battle.

They reach the core and destroy the Master Brain, which lowers the shield. The Galactic Federation begins their attack on the Doomseye. As the ship destabilizes, the Force finds themselves unable to escape the room. They are closed in, with numerous Bruisers prepared to attack, but are saved at the last minute by Samus. The Doomseye gets closer to destruction, and the Federation Force gets sucked into the vacuum of space. Prepared for death, they are saved by Samus in her Gunship and commended as heroes.